Incidence, geographical distribution and genetic diversity of sugarcane striate virus in Saccharum species in China

Plant Disease ◽  
2021 ◽  
Author(s):  
Yinfu Lin ◽  
Niyaz Ali ◽  
M. R. Hajimorad ◽  
Lijuan Zhang ◽  
Xiaohang Qi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Geographical Distribution ◽  
Phylogenetic Trees ◽  
Full Length ◽  
Leaf Sample ◽  
Local Varieties ◽  
Saccharum Spp ◽  
Saccharum Species ◽  
Germplasm Collections ◽  
Virus Incidence

A novel virus of the genus Mastrevirus, family Geminivirdae, was recently reported in sugarcane germplasm collections in Florida, Guadeloupe and Réunion, and was named sugarcane striate virus (SStrV). Although the full-length sequence of a SStrV isolate from China was obtained in 2015, the incidence, geographical distribution, and genetic diversity of this virus remained unclear. A single leaf sample from 2,368 sugarcane plants from main sugarcane producing regions of China and germplasm collections were tested for SStrV by polymerase chain reaction (PCR). Average virus incidence was 25.1% for field collected samples and SStrV was detected in most Saccharum species and two sugarcane-related species with the highest incidence in S. officinarum (44.1%) followed by Saccharum spp. local varieties (33.3%) grown for chewing cane for a long time. The virus incidence was much lower (6.8%) in modern commercial cultivars (Saccharum spp. hybrids). Phylogenetic trees based on full-length genomes of 157 SStrV isolates revealed that Chinese isolates comprised strains A and B, but not C and D that were reported in Florida, USA. SStrV strain A was the most prominent (98.7%) and widespread strain in China and was further divided into eight sub-groups. Almost half (45.6%) of the SStrV-positive samples from S. officinarum and Saccharum spp. local varieties were co-infected with sugarcane mosaic disease viruses or sugarcane yellow leaf virus. Interestingly, most of the plants infected by strain A of SStrV were asymptomatic. SStrV appears to be widespread in China, and its influence on chewing cane deserves further investigation.

Ampelographic characterization of white grapevine cul-tivars (Vitis vinifera L.) grown in Palestine

2015 ◽  
Vol 3 (1) ◽  
pp. 1-11
Author(s):  
Rezq Basheer-Salimia
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Germplasm Conservation ◽  
Genetic Distances ◽  
Vitis Vinifera L ◽  
Similarity Matrix ◽  
Breeding Programs ◽  
Local Varieties ◽  
Synonymies And Homonymies

Abstract: In Palestine, grape culture consists of ecotypes and cultivars (also called local varieties), for which a large number of homonymous and synonymous designations exist as well as misnaming of cultivars. The present study is the first report using detailed ampelographic characterizations (39 informative traits) to assess genetic diversity and detect similarities among sixteen accessions collected from putative diverse grape genotypes In general, 30 descriptors presented highly and satisfactory divergent genotypes, whereas the remaining traits showed no or very little ampelographic variation. Based on the similarity matrix and the resulting dendrogram of these ampelographic data, distinguishable genotypes as well as some cases of synonymies and homonymies clearly exist. A synonymy case seemed to be in four genotypes including Jandali-Mfarad, Jan-dali-Mrazraz, Jandali, and Hamadani-Mattar, which indeed showed genetic distances of less than 0.5, sug-gesting their relatedness, and the possibility that they are the same genotype, but with different names. In addition, homonym cases also occur in the following pairs of “Marawi’s, Hamadani’s, and Zaini’s genotypes, in which each pair seems to be two distinctive genotypes. Finally, among the 16 examined genotypes, the Zaini-Baladi genotype tended to show the highest genetic distance values from the others and thus could be potentially incorporated into any further local or regional breeding programs as well as germplasm conservation.

Prevalence and genetic diversity of viruses associated with rugose wood complex in Greek vineyards

Plant Disease ◽  
2021 ◽  
Author(s):  
Chrysoula Orfanidou ◽  
Kalliopi Moraki ◽  
Polina Panailidou ◽  
Leonidas Lotos ◽  
Asimina T Katsiani ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
First Record ◽  
Grapevine Virus ◽  
Multiple Introductions ◽  
Worldwide Distribution ◽  
Grapevine Virus A ◽  
Transmission Modes ◽  
Virus Incidence ◽  
Grapevine Virus B ◽  
Rupestris Stem Pitting

Rugose wood is one of the most important disease syndromes of grapevine and it has been associated with at least three viruses: grapevine rupestris stem pitting associated virus (GRSPaV), grapevine virus A (GVA) and grapevine virus B (GVB). All three viruses show a worldwide distribution pattern, and their genetic composition has been the focus of extensive research over the past years. Despite their first record in Greece almost 20 years ago, there is a lack of knowledge on the distribution and genetic variability of their populations in Greek vineyards. In this context, we investigated the distribution of GRSPaV, GVA and GVB in rootstocks, self-rooted and grafted grapevine cultivars, originating from different geographic regions that are representing important viticultural areas of Greece. Three new RT-PCR assays were developed for the reliable detection of GRSPaV, GVA and GVB. Our results indicated that GVA is the most prevalent in Greek vineyards, followed by GRSPaV and GVB. However, virus incidence differed among self-rooted and grafted grapevine cultivars or rootstocks tested. Selected isolates from each virus were further molecularly characterized to determine their phylogenetic relationships. All three viruses exhibited high nucleotide diversity, which was depicted in the constructed phylogenetic trees. Isolates from Greece were placed in various phylogroups, reinforcing the scenario of multiple introductions of GVA, GVB and GRSPaV in Greece and highlighting the effect of different transmission modes in the evolutionary course of the three viruses.

scholarly journals Polymorphic microsatellites of analysis in cultivars of taro

2012 ◽  
Vol 30 (1) ◽  
pp. 106-111 ◽  
Author(s):  
Raquel SC Nunes ◽  
Fernanda R Pinhati ◽  
Luciana P Golinelli ◽  
Tiyoko Nair H Rebouças ◽  
Vânia Margaret F Paschoalin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Local Varieties ◽  
Mato Grosso ◽  
Espírito Santo ◽  
Polymorphic Microsatellites ◽  
Espirito Santo ◽  
Microsatellite Alleles ◽  
Mato Grosso Do Sul ◽  
Simple Sequence

Taro (Colocasia esculenta) is a tuberous plant belonging to the Araceae family whose tuber is the 14th most consumed food crop in the world. Characterized as an unconventional vegetable, taro is grown in Brazil as a subsistence crop, but in recent years began to gain commercial importance, especially in the states of Espirito Santo, Minas Gerais and Rio de Janeiro. To avoid loss of genetic diversity of the local varieties traditionally grown in Brazil a core collection for taro germplasm has been developed by the Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural do estado do Espirito Santo (Incaper). The aim of this study was to perform a molecular characterization of the seven regional core collections. Genetic diversity of the cultivars was investigated by using SSR (Simple Sequence Repeats) polymorphisms, in seven loci (Xuqtem55, Xuqtem73, Xuqtem84, Xuqtem88, Xuqtem91, Xuqtem97 and Xuqtem110). Genetic diversity of the cultivars, based on the seven microsatellite alleles, was evaluated by using the software GelCompar II, showed that the loci Xuqtem73, Xuqtem88 and Xuqtem110 were the most informative, featuring 7, 10 and 8 alleles, respectively, a percentage of cultivars with polymorphic alleles of 85, 57 and 100% and identical PIC of 0.91. Based on Xuqtem110 locus analysis, the seven cultivars were grouped in two clusters. Chinês Regional Incaper cultivar was originated from Chinês cultivar which originated the São Bento cultivar, corroborating previous results. Macaquinho and Chinês cultivars were shown to be the primitive ones originating the allelic collections found in the states of Mato Grosso do Sul and Espirito Santo.

scholarly journals Whole genome sequencing reveals the genomic diversity, taxonomic classification, and evolutionary relationships of the genus Nocardia

2021 ◽  
Vol 15 (8) ◽  
pp. e0009665
Author(s):  
Shuai Xu ◽  
Zhenpeng Li ◽  
Yuanming Huang ◽  
Lichao Han ◽  
Yanlin Che ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Gene Families ◽  
Single Copy ◽  
Taxonomic Classification ◽  
Genomic Diversity ◽  
Evolutionary Relationships ◽  
Taxonomic Structure ◽  
Pan Genome ◽  
Dipeptidyl Aminopeptidase

Nocardia is a complex and diverse genus of aerobic actinomycetes that cause complex clinical presentations, which are difficult to diagnose due to being misunderstood. To date, the genetic diversity, evolution, and taxonomic structure of the genus Nocardia are still unclear. In this study, we investigated the pan-genome of 86 Nocardia type strains to clarify their genetic diversity. Our study revealed an open pan-genome for Nocardia containing 265,836 gene families, with about 99.7% of the pan-genome being variable. Horizontal gene transfer appears to have been an important evolutionary driver of genetic diversity shaping the Nocardia genome and may have caused historical taxonomic confusion from other taxa (primarily Rhodococcus, Skermania, Aldersonia, and Mycobacterium). Based on single-copy gene families, we established a high-accuracy phylogenomic approach for Nocardia using 229 genome sequences. Furthermore, we found 28 potentially new species and reclassified 16 strains. Finally, by comparing the topology between a phylogenomic tree and 384 phylogenetic trees (from 384 single-copy genes from the core genome), we identified a novel locus for inferring the phylogeny of this genus. The dapb1 gene, which encodes dipeptidyl aminopeptidase BI, was far superior to commonly used markers for Nocardia and yielded a topology almost identical to that of genome-based phylogeny. In conclusion, the present study provides insights into the genetic diversity, contributes a robust framework for the taxonomic classification, and elucidates the evolutionary relationships of Nocardia. This framework should facilitate the development of rapid tests for the species identification of highly variable species and has given new insight into the behavior of this genus.

scholarly journals Genetic Diversity Analysis of Indonesian Pigmented Rice Accessions Based on Functional Molecular Markers

2021 ◽  
Vol 17 (1) ◽  
pp. 25
Author(s):  
Andari Risliawati ◽  
Yusi N. Andarini ◽  
Rerenstradika T. Terryana ◽  
Kristianto Nugroho ◽  
Puji Lestari
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Gene Bank ◽  
Diversity Analysis ◽  
Anthocyanin Content ◽  
Local Varieties ◽  
Pigmented Rice ◽  
Health Studies ◽  
Pericarp Color ◽  
Functional Molecular Markers

Pigmented rice is functional staple food that becomes popular because of its anthocyanin content which is beneficial for health. Studies on the diversity of the local variety of Indonesian pigmented rice accessions have been carried out, but are still limited to one region of germplasm origin. This study aimed to analyze the genetic diversity of local varieties of pigmented rice collections of the IAARD-ICABIOGRAD Gene Bank. A total of 93 pigmented rice accessions from 16 provinces in Indonesia were analyzed using 15 functional molecular markers of SSR, STS, and indel. The total alleles detected were 115 with an average per locus of genetic diversity value of 0.71. There were five markers with PIC values >0.75, i.e. RM167, RM223, R8M33, R10M10, and GBSS1. The accessions were divided into two main groups based on their pericarp color. It is necessary to analyze the physicochemical content of the local rice accessions to complement the existing diversity information and identify potential pigmented rice accessions with high palatability.

scholarly journals Single Nucleotide Polymorphisms and Indel Markers from the Transcriptome of Garlic

2016 ◽  
Vol 141 (1) ◽  
pp. 62-65 ◽  
Author(s):  
Michael J. Havey ◽  
Yul-Kyun Ahn
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Characteristics ◽  
Single Nucleotide ◽  
Germplasm Collections ◽  
Indel Markers ◽  
Production Environments ◽  
Culinary Uses

Garlic (Allium sativum) is cultivated worldwide and appreciated for its culinary uses. In spite of primarily being asexually propagated, garlic shows great morphological variation and adaptability to diverse production environments. Molecular markers and phenotypic characteristics have been used to assess the genetic diversity among garlics. In this study, we undertook transcriptome sequencing from a single garlic plant to identify molecular markers in expressed regions of the garlic genome. Garlic sequences were assembled and selected if they were similar to monomorphic sequences from a doubled haploid (DH) of onion (Allium cepa). Single nucleotide polymorphisms (SNPs) and insertion–deletion (indel) events were identified in 4355 independent garlic assemblies. A sample of the indels was verified using the original complementary DNA (cDNA) library and genomics DNAs from diverse garlics, and segregations confirmed by sexual progenies of garlic. These molecular markers from the garlic transcriptome should be useful for estimates of genetic diversity, identification and removal of duplicate accessions from germplasm collections, and the development of a detailed genetic map of this important vegetable crop.

scholarly journals Research Concerning Cucumber (Cucumis Sativus L. Mill) Genetic Diversity

2011 ◽  
Vol 68 (2) ◽  
Author(s):  
Aurel MAXIM ◽  
Mignon ŞANDOR ◽  
Lucia MIHALESCU ◽  
Ovidiu MAXIM ◽  
Oana MARE ROŞCA
Keyword(s):  
Genetic Diversity ◽  
Biological Diversity ◽  
Genetic Erosion ◽  
Farming Systems ◽  
Convention On Biological Diversity ◽  
Cultivated Plants ◽  
Cucumis Sativus L ◽  
Local Varieties ◽  
Industrial Farming ◽  
The University

During the second part of the twentieth century the cultivated plants have been faced with genetic erosion, because of the expandinding industrial farming systems. The sustainable agriculture can not exist without a rich genetic diversity. After the United Nations Conference from Rio de Janeiro (1992), when the Convention on Biological Diversity was adopted, a series of acts and european references that protect agrobiodiversity had emerged. Between 2007 and 2010, at the University of Agricultural Sciences and Veterinary Medicine a program which aims to identify and conserve local vegetable varieties was conducted. Out of 290 cultivars, 171 (58.9%) were genuine local varieties. There were collected 12 cucumber cultivars from the following counties: Salaj (7), Cluj (3), Bistrita-Nasaud (1) and Satu-Mare (1). The morphologic caractheristics proved that all this 12 cultivars were authentic and valuable local varieties. The local varieties were agronomical, biological and biochemical characterized, both in field and laboratory. The seeds achieved from those 12 local varieties were preserved in the Suceava Gene Bank, from where stakeholders (farmers, agronomists, researchers) can obtain seeds.

Analisis Keragaman Genetik 28 Nomor Koleksi Kakao (Theobroma cacao L.) Berdasarkan Marka SSR

2017 ◽  
Vol 4 (1) ◽  
pp. 13 ◽  
Author(s):  
Ilham Nur ardhi Wicaksono ◽  
Rubiyo Rubiyo ◽  
Dewi Sukma ◽  
Sudarsono Sudarsono
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Plant Molecular Biology ◽  
Average Value ◽  
Germplasm Collections ◽  
Ctab Method ◽  
Parental Lines ◽  
Biology Laboratory ◽  
Superior Clones ◽  
Selection Of

<em>Analysis of genetic diversity of cacao germplasm collections using molecular markers has an important role in the assembly of new superior clones. The availability of commercial and superior local clones could increase the success of new superior clones’ assembly. Hence, the genetic diversity analysis of these materials needs to be done. The study was aimed to analyze genetic diversity of 28 cacao collections based on SSR markers that would be useful for selection of parental lines. The research was conducted in the Integrated Laboratory, Indonesian Industrial and Beverage Crops Research Institute, Sukabumi, and Plant Molecular Biology laboratory, Bogor Agricultural University, from November 2015 to May 2016.</em> <em>Analysis of genetic diversity was conducted using 28 cacao clones (13 superior local clones and 15 commercial clones). DNA was extraction using CTAB method, which then amplified by PCR technique using 20 SSR primers. The result showed that all SSR markers used in this study were polymorphic with an average value of PIC was high (57%). Phylogenetic tree constructed using DARwin program version 6.05 is divided into 3 major groups, which placed commercial and superior local clones together in each group. Superior local clones observed herein might have close relationships with commercial clones that have long been cultivated in Indonesia. Furthermore, some cacao clones could potentially be parental lines because they had high genetic distance. The results showed that SSR markers are powerful tools to determine potential parental lines, which is expected to increase the chances of heterosis in their progenies.</em>

KERAGAMAN FENOTIPE DAN GENETIK TIGA VARIETAS KELAPA GENJAH KOPYOR ASAL PATI JAWA TENGAH

2016 ◽  
Vol 21 (1) ◽  
pp. 1 ◽  
Author(s):  
ISMAIL MASKROMO ◽  
ELSJE T. TENDA ◽  
MEITY A. TULALO ◽  
HENGKY NOVARIANTO ◽  
DEWI SUKMA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Molecular Biology ◽  
Plant Molecular Biology ◽  
Morphological Diversity ◽  
Local Varieties ◽  
Central Java ◽  
Variety Selection ◽  
Ssr Loci ◽  
Biology Laboratory

<p>ABSTRAK<br />Kelapa Genjah kopyor asal Pati, Jawa Tengah merupakan<br />kekayaaan hayati asli Indonesia dengan nilai ekonomi tinggi. Informasi<br />keragaman genetik kelapa kopyor masih terbatas. Data keragaman<br />morfologi dan genetik diperlukan dalam program pemuliaan kelapa<br />kopyor. Penelitian ini mempelajari keragaman tiga varietas kelapa genjah<br />kopyor asal Pati yang telah dilepas berdasarkan karakter morfologi,<br />kuantitas endosperma, dan keragaman alel marka SSR. Penelitian<br />dilakukan di Pati dan di Laboratorium Plant Molecular Biology,<br />Departemen Agronomi dan Hortikultura, IPB. Evaluasi dilakukan terhadap<br />tiga populasi kelapa Genjah kopyor (hijau, coklat, dan kuning) dengan 30<br />tanaman sampel untuk setiap populasi. Rataan data morfologi digunakan<br />untuk menyusun dendogram. Kuantitas endosperma diamati pada satu<br />buah kelapa kopyor per tanaman yang dievaluasi. Karakteristik<br />endosperma dikelompokkan sesuai kategori yang telah ditetapkan. Untuk<br />setiap populasi, analisis marka dengan lima pasang primer SSR dilakukan<br />pada 10 tanaman sampel. Data yang didapat digunakan untuk menentukan<br />keragaman genetik kelapa Genjah kopyor asal Pati. Hasil pengamatan<br />menunjukkan keragaman morfologis dan alel SSR antar tanaman dalam<br />varietasnya (keragaman intra-varietas) rendah. Sebaliknya, keragaman<br />morfologis dan alel SSR antar varietasnya tinggi. Kuantitas endosperma<br />kelapa Genjah kopyor asal Pati bervariasi antara skor 1–6. Keragaman<br />genetik yang rendah dalam varietas dan tinggi antar ketiga varietas (coklat,<br />hijau, dan kuning) memperkuat pelepasan ketiganya sebagai varietas lokal.<br />Selain itu, keragaman genetik antar tanaman dalam varietas yang rendah<br />mendukung penggunaan ketiga varietas lokal sebagai tetua dalam program<br />perakitan varietas kelapa kopyor unggul baru. Tetua yang dipilih dapat<br />diseleksi intra-varietas berdasarkan persentase buah kopyor per tandan<br />dan skor kuantitas endosperma yang tinggi.<br />Kata kunci: Keragaman morfologis, keragaman intra dan antar varietas,<br />kuantitas endosperma</p><p>ABSTRACT<br />Kopyor dwarf coconuts are mutants from Pati, Central Java having<br />high economic values. However, morphological and genetic diversities of<br />this coconut were still limited. Morphological and genetic diversity data<br />are needed for breeding program. The research objectives were to evaluate<br />intra and inter-specific diversity based on morphology, endosperm<br />quantity, and SSR alleles. Field evaluations were conducted in Pati while<br />laboratory activities were at Plant Molecular Biology Laboratory,<br />Department of Agronomy and Horticulture, IPB. Three populations of<br />kopyor dwarf varieties (brown, green, and yellow) were evaluated. Thirty<br />trees were sampled for each population. The average of morphological<br />data were used to construct cluster analysis. Endosperm quantity was<br />scored (0 – 9) based on a single nut sample. Ten palms were analyzed<br />using five SSR loci for each population and used to determine genetic<br />diversity of populations. Results of observations indicated intra-variety<br />morphological and SSR allele variations among kopyor dwarf was low.<br />However, inter-variety variations were high. The endosperm quantity<br />scores among kopyor dwarf coconut ranged from 1–6. The low intra-<br />variety and high inter-variety variations among the three kopyor dwarf<br />coconut supported their release as different local varieties. Moreover, the<br />low intra-variety phenotypic and genotypic diversities among kopyor<br />brown, green, and yellow dwarf coconut support their use as parents for<br />new and superior kopyor coconut variety development in the future. For<br />such purpose, however, it is necessary to conduct intra-variety selection to<br />identify desirable parents based on high kopyor fruit percentage per bunch<br />and for high kopyor endosperm quantity.<br />Key words: Morphological diversity, intra and inter variety diversities,<br />quantity, endosperm</p>

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